Definitely give Linux it's own drive. Windows has the tendency to wreck perfectly good Linux partitions when installed after it or if it ever needs to be reinstalled. A separate drive can safely be unplugged while Windows does its thing.
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If you ever have a bootloader problem, Super-Grub-2 CD is epic. I broke the boot loader on my most important server (Proxmox one) once, and I would have probably had to reinstall Linux without Super-Grub-2.
THING TO REMEMBER ABOUT SSDS:
DO NOT MAKE A SWAP FILE ON AN SSD. DO NOT. JUST DONT. ITS A BAD IDEA.
Choose "Something Else" for your partitioning in a Linux installer, and make sure there's no swap. Use a normal HDD for swap.
Take a clonezilla image of your disks before you go install Linux. :)
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Yeah I was considering this route and making it swappable via one of the front drive bays.
Its going well everyone. Thanks making this thread active.
The only major problem I am having is with my 3TB HDD. Its NTFS with GPT to get the full 3TB. I'll take a detailed look into it after work but it seems Lunix can only interact with it in a 'read-only' manner, which rules out playing Don't Starve. I'm definitely taking @Aryvandaar 's advice backing ip before I mess with it. I'm vaguely aware of UDF. In any case I'm grateful for suggestions on Universal file systems or partitioning my HDD (not ideal).
(Also I have to set up both displays everytime linux boots. Ie doesn't save position non-volatile)
I believe you can get write access if you install the ntfs-3g library - however, I don't think you can execute binaries from ntfs at all in Linux, so that would be useless for you anyways.